Given a Seurat object containing Kandinsky data, this function will modify the neighbour network generated by Kandinsky according to new conditions specified by the user.
nb_update(
seurat = NULL,
nb.method = c("K", "C", "D", "M", "Q"),
snap = NULL,
layers = 1,
d.max = 20,
k = 10,
soi = F
)a Seurat object containing Kandinsky data slot
character string specifying the method to be used to create a `nb` neighbour object. Must be one of the following: 'Q': queen contiguity method,check for contact (not overlap) between any edge or side od two polygons (refers to the queen movement rule in chess). Currently only applicable for Visium/Visium-HD data 'C': centroid-based method, use maximum centroid distance threshold to identify spot/cell neighbours 'D': Delaunay triangulation 'K': KNN method, define k closest neighbours to each spot/cell 'M': membrane-based method, check for the occurrence of a physical contact/intersection within a distance threshold between cell boundaries. Not applicable in the case of Visium spots.
numeric, maximum accepted distance between Visium spots or Visium-HD bins to define contiguity relationships. Only Applied when `nb.method = Q`.
numeric, number of concentric contiguous layers to include in spot neighbourhood. Only Applied when `nb.method = Q`. Default is 1
numeric, maximum distance accepted between polygon centroids to define neighbour relation
numeric, number of nearest neighbour to select with knn algorithm
boolean, whether or not filter Delaunay network to keep sphere of influence (SOI) graph. Default is FALSE
seurat object with updated 'nb' neighbours in Kandinsky data
Other nb_funcs:
centroid_nb(),
knn_nb(),
membrane_nb(),
nb_expand(),
queen_nb(),
tri_nb()